/usr/share/syrthes/syrthes.py is in syrthes 4.3.0-dfsg1-2build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# syrthes.py V4.0.0-12b
import os
import os.path
import sys
import re
import shutil
import datetime
import fnmatch
import subprocess
from optparse import OptionParser
from time import gmtime, strftime
# Global environnement variables
s4home = None
arch = None
mpidir = None
#
syrthes_pp = None
syrthes_ppfonc = None
syrthes_post = None
syrthes_ensight = None
syrthes_med = None
#
# *************************
# BEGIN OF CLASS DEFINITION
# *************************
#-------------------------------------------------------------------------------
# Definition of a class for managing Syrthes case
#-------------------------------------------------------------------------------
class SyrthesCase:
def __init__(self, name = None,
data_file = "syrthes_data.syd",
case_dir = None,
data_dir = None,
exec_dir = None,
src_dir = None,
n_procs = 1,
n_procs_ray = -1,
part_tool_name ="metis",
prepro = True,
post_mode = None,
debug = False,
logfile = None):
"""
Initialize the structure for a Syrthes computation
"""
self.n_procs = n_procs # Number of processes for syrthes computation
self.n_procs_ray = n_procs_ray # Number of processes for computing radiative transfer
self.part_tool_name = part_tool_name # name of the partitionning tool
self.prepro = prepro # Do preprocessing
self.parall = False # Parallel run ?
self.param = None # Parameters defined in data_file (SyrParam object)
self.post_mode = post_mode # King of post-processing format (None, Ensight, MED)
self.debug = debug
self.c_mesh_dir = None # Will be set while reading param file
self.c_mesh_name = None # Will be set while reading param file
self.r_mesh_dir = None # Will be set while reading param file
self.r_mesh_name = None # Will be set while reading param file
self.resu_dir = None # Will be set while reading param file
# Case directory
if case_dir != None:
self.case_dir = case_dir
else:
case_dir = os.path.dirname(data_file)
if os.path.isabs(case_dir):
self.case_dir = case_dir
else:
self.case_dir = os.path.abspath(case_dir)
self.data_file = os.path.basename(data_file)
# Execution directory
if exec_dir == None or len(exec_dir) == 0:
self.exec_dir = self.case_dir
else:
if os.path.isabs(exec_dir):
self.exec_dir = exec_dir
else:
self.exec_dir = os.path.abspath(exec_dir)
# Data directory (data file, input user data files, ...)
if data_dir != None:
if os.path.isabs(data_dir):
self.data_dir = data_dir
else:
self.data_dir = os.path.abspath(data_dir)
else:
self.data_dir = self.case_dir
# Sources directory (user subroutines, Makefile)
if src_dir == None or len(src_dir) == 0:
self.src_dir = self.case_dir
else:
if os.path.isabs(src_dir):
self.src_dir = src_dir
else:
self.src_dir = os.path.abspath(src_dir)
# Post-processing directory
self.post_dir = os.path.join(self.exec_dir, 'POST')
# Partionning directory
if self.n_procs > 1:
self.part_dir = os.path.join(self.exec_dir, 'PART')
else:
self.part_dir = None
# Syrthes Case name
if name == None or len(name) == 0:
name = os.path.basename(self.case_dir)
self.name = name
# Coupling parameters
if self.n_procs > 1:
self.parall = True
# Update data_dile
if self.n_procs > 1:
self.update_datafile = True
else:
self.update_datafile = False
# Output
self.logfile = logfile # Output filename
self.echo = False # Redirection or not of the output into a file
if logfile != None:
self.echo = True
#---------------------------------------------------------------------------
def set_exec_dir(self, exec_dir):
self.exec_dir = exec_dir
# Post-processing directory
self.post_dir = os.path.join(self.exec_dir, 'POST')
# Partionning directory
if self.n_procs > 1:
self.part_dir = os.path.join(self.exec_dir, 'PART')
else:
self.part_dir = None
# Data directory (data file, input user data files, ...)
if self.data_dir == None or len(self.data_dir) == 0:
self.data_dir = self.exec_dir
# Sources directory (user subroutines, Makefile)
if self.src_dir == None or len(self.src_dir) == 0:
self.src_dir = self.exec_dir
#---------------------------------------------------------------------------
def set_src_dir(self, src_dir, force = True):
# Sources directory (user subroutines, Makefile)
if self.src_dir == None or len(self.src_dir) == 0:
self.src_dir = src_dir
else:
if force == True:
self.src_dir = src_dir
#---------------------------------------------------------------------------
def set_data_dir(self, data_dir, force = True):
# Data directory (data file, input user data files, ...)
if self.data_dir == None or len(self.data_dir) == 0:
self.data_dir = data_dir
else:
if force == True:
self.data_dir = data_dir
#---------------------------------------------------------------------------
def set_n_procs(self, n_procs):
self.n_procs = int(n_procs)
if self.n_procs > 1:
self.parall = True # Parallel run to do
if self.part_dir == None or len(self.part_dir) == 0:
self.part_dir = os.path.join(self.exec_dir, 'PART')
#---------------------------------------------------------------------------
def set_logfile(self, logfile_name):
self.logfile = str(logfile_name)
self.echo = True
#---------------------------------------------------------------------------
def read_data_file(self):
self.param = read_syrthes_param(os.path.join(self.case_dir,
self.data_file))
# Define self.c_mesh_dir and self.c_mesh_name
self.c_mesh_name = os.path.basename(self.param.c_mesh_name)
if os.path.dirname(self.param.c_mesh_name)[0:2] == "C:" : # convertir format de chemin Windows en cygwin
dirname_formatcygwin = os.path.dirname(self.param.c_mesh_name).replace('C:', '/cygdrive/c', 1)
c_mesh_dir = os.path.join(self.case_dir, dirname_formatcygwin)
else :
c_mesh_dir = os.path.join(self.case_dir, os.path.dirname(self.param.c_mesh_name))
if os.path.isabs(c_mesh_dir):
self.c_mesh_dir = c_mesh_dir
else:
self.c_mesh_dir = os.path.abspath(c_mesh_dir)
if self.c_mesh_dir != self.exec_dir:
self.update_datafile = True
if self.c_mesh_dir != c_mesh_dir:
self.update_datafile = True
# Define self.r_mesh_dir and self.r_mesh_name if needed
if self.param.r_mesh_name != None and len(self.param.r_mesh_name) > 0:
self.r_mesh_name = os.path.basename(self.param.r_mesh_name)
if os.path.dirname(self.param.r_mesh_name)[0:2] == "C:" : # convertir format de chemin Windows en cygwin
dirname_formatcygwin = os.path.dirname(self.param.r_mesh_name).replace('C:', '/cygdrive/c', 1)
r_mesh_dir = os.path.join(self.case_dir, dirname_formatcygwin)
else :
r_mesh_dir = os.path.join(self.case_dir, os.path.dirname(self.param.r_mesh_name))
if os.path.isabs(r_mesh_dir):
self.r_mesh_dir = r_mesh_dir
else:
self.r_mesh_dir = os.path.abspath(r_mesh_dir)
if self.r_mesh_dir != self.exec_dir:
self.update_datafile = True
if self.r_mesh_dir != r_mesh_dir:
self.update_datafile = True
# isabelle
# Define self.result_dir and self.result_name
self.result_name = os.path.basename(self.param.result_name)
if os.path.dirname(self.param.result_name)[0:2] == "C:" : # convertir format de chemin Windows en cygwin
dirname_formatcygwin = os.path.dirname(self.param.result_name).replace('C:', '/cygdrive/c', 1)
result_dir = os.path.join(self.case_dir, dirname_formatcygwin)
else :
result_dir = os.path.join(self.case_dir, os.path.dirname(self.param.result_name))
if os.path.isabs(result_dir):
self.result_dir = result_dir
else:
self.result_dir = os.path.abspath(result_dir)
if self.result_dir != self.exec_dir:
self.update_datafile = True
if self.result_dir != result_dir:
self.update_datafile = True
# In case of code coupling -> update data file
# isabelle
if self.param.coupling == True:
self.result_dir = self.exec_dir
self.update_datafile = True
#---------------------------------------------------------------------------
def logfile_init(self):
if self.echo == True:
date=strftime("%a, %d %b %Y %H:%M:%S", gmtime())
self.logfile = os.path.join(self.exec_dir, os.path.basename(self.logfile))
os.system('echo ' + date + ' > ' + self.logfile)
#---------------------------------------------------------------------------
def clean(self):
dir_files = os.listdir(os.getcwd())
tmp1 = ['tmp.data', 'compile.log', 'listsyr', 'listing',
'syrthes.log', 'syrthes', 'user_fct.c']
tmp2 = fnmatch.filter(dir_files, '*~')
tmp = tmp1 + tmp2
for t in tmp:
if os.access(os.path.join(self.exec_dir, t), 6) == 1:
os.remove(os.path.join(self.exec_dir, t))
#---------------------------------------------------------------------------
def interpret_func(self, dest = None):
# Check syrthes environment and set paths
if s4home == None:
retval = check_and_load_env()
if retval != 0:
err = '\n Error during checking and loading environment.\n'
sys.stderr.write(err)
return 1
cur_dir = os.getcwd()
os.chdir(self.case_dir)
if self.param == None:
err = '\n Try to use data from SYRTHES data file\n' \
' but this file was not read yet !\n -> Error !\n'
sys.stderr.write(err)
sys.exit('Stop.')
if self.param.interpreted_func == True:
sys.stdout.write(' \nBuilding user functions..\n')
cmd = syrthes_ppfonc + ' -d ' + self.data_file
if self.echo == True:
ret = os.system(cmd + ' >> ' + self.logfile)
else:
ret = os.system(cmd)
if dest == None:
dest = self.src_dir
if dest != self.case_dir:
shutil.move(os.path.join(self.case_dir, 'user_fct.c'),
os.path.join(dest, 'user_fct.c'))
# Comme back to initial directory
os.chdir(cur_dir)
#---------------------------------------------------------------------------
def prepare_run(self,
exec_srcdir = None,
compile_logname = None):
"""
Create execution directory if needed
Copy data files, source files into execution directory if needed
exec_srcdir: source files directory in execution directory
by default it is the same place (not true in cfd coupling mode)
"""
retval = 0
# Check syrthes environment and set paths
if s4home == None:
retval = check_and_load_env()
if retval != 0:
err = '\n Error during checking and loading environment.\n'
sys.stderr.write(err)
return 1
# Sanity checks
retval = check_and_create_dir(self.exec_dir)
if retval != 0:
err = '\n Error during check/create directory: ' + self.exec_dir + '\n'
sys.stderr.write(err)
return 1
# Clean execution directory before computation
self.clean()
# Treament of interpreted functions
self.interpret_func(dest = exec_srcdir)
# Copy source files into exec_srcdir
# ----------------------------------
src_files = []
if self.src_dir != exec_srcdir and exec_srcdir != None:
srcdir_files = os.listdir(self.src_dir)
src_files = (fnmatch.filter(srcdir_files, '*.c')
+ fnmatch.filter(srcdir_files, 'Makefile'))
if len(src_files) > 0:
# Add header files to list so as not to forget to copy them
src_files = src_files + fnmatch.filter(srcdir_files, '*.h')
# Copy source files to execution directory
if (self.exec_dir != exec_srcdir):
retval = check_and_create_dir(exec_srcdir)
if retval != 0:
err = '\n Error during check/create directory: '
err += self.exec_dir + '\n'
sys.stderr.write(err)
return 1
for f in src_files:
src_file = os.path.join(self.src_dir, f)
dest_file = os.path.join(exec_srcdir, f)
shutil.copy2(src_file, dest_file)
self.src_dir = exec_srcdir
# Compile and build syrthes
# -------------------------
retval = build_syrthes(parall = self.parall,
cfd_coupling = self.param.coupling,
fname = compile_logname,
debug = self.debug,
srcdir = self.src_dir,
destdir = self.exec_dir)
if retval != 0:
err = '\n Error during building syrthes executable.\n'
sys.stderr.write(err)
return 2
# Copy syrthes data file if needed
# --------------------------------
if self.case_dir != self.exec_dir:
src = os.path.join(self.case_dir, self.data_file)
dst = os.path.join(self.exec_dir, self.data_file)
if not os.path.isfile(src) and not os.path.islink(src):
err = src + ' is not a regular file or link.\n -> Error !\n'
sys.stderr.write(err)
return 1
shutil.copy2(src, dst)
# Copy all user data files from data_dir to exec_dir
# --------------------------------------------------
if self.data_dir != self.exec_dir:
# In case: data_dir = src_dir but data_dir != exec_dir
lst = os.listdir(self.data_dir)
exclude = ['tmp.data', 'syrthes', 'syrthes.py', self.c_mesh_name,
'syrthes_data.syd_example', 'listing', 'listsyr',
'syrthes.log', self.data_file]
exclude.append(src_files)
if self.r_mesh_name != None and len(self.r_mesh_name) > 0:
exclude.append(self.r_mesh_name)
for e in exclude:
if e in lst:
lst.remove(e)
for f in lst:
src = os.path.join(self.data_dir, f)
if not os.path.isdir(src):
dst = os.path.join(self.exec_dir, f)
shutil.copy2(src, dst)
self.data_dir = self.exec_dir
return retval
#---------------------------------------------------------------------------
def preprocessing(self):
print ""
print " ---------------------------"
print " Start SYRTHES preprocessing"
print " ---------------------------"
print ""
os.chdir(self.exec_dir)
# Check syrthes environment and set paths
if s4home == None:
retval = check_and_load_env()
if retval != 0:
err = '\n Error during checking and loading environment.\n'
sys.stderr.write(err)
return 1
retval = 0
if self.n_procs > 1: # Parallel run => first, mesh partitionning
retval = check_and_create_dir(self.part_dir)
if retval != 0:
return retval
if self.param == None:
err = '\n Try to use data from SYRTHES data file\n' \
' but this file was not read yet !\n -> Error !\n'
sys.stderr.write(err)
sys.exit('Stop.')
# Partionning
# -----------
# Modify mesh prefix to put partionned mesh into PART directory
new_c_mesh_prefix = os.path.basename(self.param.c_mesh_prefix)
new_c_mesh_prefix = os.path.join('PART', new_c_mesh_prefix)
if self.prepro == True:
sys.stdout.write('Pre-processing SYRTHES files.. \n')
cmd = syrthes_pp + ' -v '+' -n '+ str(self.n_procs)
cmd += ' --toolpart ' + self.part_tool_name
cmd += ' -m '+ '"' + os.path.join(self.c_mesh_dir, self.c_mesh_name) + '"'
cmd += ' -d ' + '"' + self.data_file + '"' + ' -o ' + '"'+new_c_mesh_prefix+'"'
sys.stdout.write(' --> ' + cmd +'\n')
if self.echo:
retval = os.system(cmd + ' >> '+ self.logfile)
else:
retval = os.system(cmd)
if retval != 0:
return retval
else:
sys.stdout.write(' -> OK\n\n')
# Update mesh name in data file
if self.update_datafile == True:
sys.stdout.write('Updating the mesh file name.. \n')
try:
if self.data_file != None or len(self.data_file) > 0:
if self.n_procs > 1 and self.prepro == True:
new_abs_c_mesh_name = os.path.join(self.part_dir, self.c_mesh_name)
else:
new_abs_c_mesh_name = os.path.join(self.c_mesh_dir, self.c_mesh_name)
if self.r_mesh_dir != None and self.r_mesh_name != None:
new_abs_r_mesh_name = os.path.join(self.r_mesh_dir, self.r_mesh_name)
else:
new_abs_r_mesh_name = None
if self.param.restart == True:
new_abs_restart = os.path.join(self.case_dir, self.param.restart_file)
else:
new_abs_restart = None
retval = self.param.update(self.n_procs,
new_abs_c_mesh_name,
new_abs_r_mesh_name,
new_abs_restart,
new_filename = "tmp.data")
self.data_file = "tmp.data"
else:
sys.stderr.write('\n Data file not defined.\n')
sys.stderr.write(' Error while updating the mesh file name !\n')
retval = 1
except:
sys.stderr.write('\n Error while updating the mesh file name !\n')
retval = 1
else:
sys.stdout.write(' -> OK\n\n')
return retval
#---------------------------------------------------------------------------
def build_cmdline(self):
cmd = ''
mpi_env=[None, None, None] # Start script, Run script, Finalize script
if self.n_procs > 1: # Parallel run
# Test if mpi library is MPICH2 or OPENMPI (otherwise exit with error)
# MPI launcher
mpi_bindir=os.path.join(mpidir, 'bin')
# Update mpi_env with start script
mpistart=os.path.join(mpi_bindir,'mpdboot')
if os.path.isfile(mpistart) or os.path.islink(mpistart):
mpi_env[0] = mpistart
# Update mpi_env with run script
mpiexec=os.path.join(mpi_bindir,'mpiexec')
if os.path.isfile(mpiexec) or os.path.islink(mpiexec):
mpi_env[1] = mpiexec
else:
err=' ' + str(mpiexec)+ ' is not a valid file\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution')
# Update mpi_env with finalize script
mpiexit=os.path.join(mpi_bindir,'mpdallexit')
if mpi_env[0] != None:
if os.path.isfile(mpiexit) or os.path.islink(mpiexit):
mpi_env[2] = mpiexit
else:
err= 'MPICH2 implementation found but not mpdallexit\n'
err+= 'mpipath used: ' + mpi_bindir
sys.stderr.write(err)
sys.exit('Stop Syrthes execution')
else:
mpi_env[2] = None
if mpi_env[0] != None:
cmd += mpi_env[0] + ' && '
cmd += mpi_env[1] + ' -n ' + str(self.n_procs)
cmd += ' ./syrthes -d ' + self.data_file
if self.n_procs_ray > 0:
cmd += ' -r ' + str(self.n_procs_ray)
if self.logfile != None:
cmd += ' --log ' + str(self.logfile)
if mpi_env[2] != None:
cmd += ' && ' + mpi_env[2]
return cmd
#---------------------------------------------------------------------------
def run(self):
if not os.path.isdir(self.exec_dir):
err = '\n Execution directory is not a directory!\n' \
' -> Error !\n'
sys.stdout.write(err)
return 1
os.chdir(self.exec_dir)
if self.param.coupling == True:
err = '\n Cannot run syrthes in code coupling mode with this function.\n'
sys.stderr.write(err)
return 1
# Build command line
msg = 'Execution of SYRTHES.. \n'
msg += ' -> number of processors for conduction = ' + str(self.n_procs) + ' \n'
if (self.n_procs_ray > 0):
msg += ' -> number of processors for radiation = ' + str(self.n_procs_ray)
msg += ' (if needed only: see SYRTHES data file) \n'
sys.stdout.write(msg)
if (self.n_procs_ray > 0 and self.n_procs_ray > self.n_procs):
err=' Number of proc. for radiation > Number of proc. for conduction\n'
err+=' This is not possible.\n'
err+=' Stop Syrthes execution'
sys.stderr.write(err)
return 1
cmd = self.build_cmdline()
# Execution of syrthes
try:
if self.echo == True:
ret = os.system(cmd +' >> ' + self.logfile)
else:
ret = os.system(cmd)
except:
ret = 1
return ret
#---------------------------------------------------------------------------
def postprocessing(self, mode = 'ens'):
sys.stdout.write('Post-processing.. \n')
# Check syrthes environment and set paths
if s4home == None:
retval = check_and_load_env()
if retval != 0:
err = '\n Error during checking and loading environment.\n'
sys.stderr.write(err)
return 1
retval = check_and_create_dir(self.post_dir)
if retval != 0:
return retval
if self.n_procs > 1: # Additional treatment for a parallel run
if not os.path.isdir(self.part_dir):
err = '\n Partition directory is not a directory!\n' \
' -> Error !\n'
sys.stdout.write(err)
return 1
# isabelle
if self.prepro:
mesh_path = os.path.join(self.part_dir, self.c_mesh_name)
else:
mesh_path = os.path.join(self.c_mesh_dir, self.c_mesh_name)
resu_path = os.path.join(self.part_dir, self.result_name + '.res')
rdt_path = os.path.join(self.part_dir, self.result_name + '.rdt')
rdt_path0 = os.path.join(self.part_dir, self.result_name + '_part00000.rdt')
merge_path = os.path.join(self.result_dir, self.result_name + '_all')
cmd = syrthes_post + ' -n ' + str(self.n_procs) + ' -m '+ '"'+ mesh_path +'"'
cmd += ' -r ' + '"'+resu_path+'"' + ' -o ' + '"'+merge_path+'"'
cmdrdt = syrthes_post + ' -n ' + str(self.n_procs) + ' -m '+ '"'+ mesh_path +'"'
cmdrdt += ' -r ' + '"'+rdt_path+'"' + ' -o ' + '"'+merge_path+'"'
try:
sys.stdout.write(' .merging data.. (.res) --> _all.res \n')
sys.stdout.write(' --> ' + cmd +'\n')
if self.echo:
retval = os.system(cmd + ' >> ' + self.logfile)
else:
retval = os.system(cmd)
if (os.path.isfile(rdt_path0)):
sys.stdout.write(' .merging data.. (.rdt) --> _all.rdt \n')
sys.stdout.write(' --> ' + cmd +'\n')
if self.echo:
retval = os.system(cmdrdt + ' >> ' + self.logfile)
else:
retval = os.system(cmdrdt)
except:
err = ' Cannot execute tool to merge results for post-processing\n'
err += ' -> Error !\n'
sys.stderr.write(err)
return 1
else:
if retval != 0:
return retval
else:
# isabelle
mesh_path = os.path.join(self.result_dir, self.result_name + '_all.syr')
resu_path = os.path.join(self.result_dir, self.result_name + '_all.res')
rdt_path = os.path.join(self.result_dir, self.result_name + '_all.rdt')
output = self.result_name + '_all'
outputrdt = self.result_name + '_rdt_all'
else: # Serial run
mesh_path = os.path.join(self.c_mesh_dir, self.c_mesh_name)
# isabelle
resu_path = os.path.join(self.result_dir, self.result_name + '.res')
rdt_path = os.path.join(self.result_dir, self.result_name + '.rdt')
output = self.result_name
outputrdt = self.result_name + '_rdt'
# result file
if mode == 'ens':
# Execute syrthes -> ensight tool
sys.stdout.write(' .syrthes (.res) --> ensight... \n')
cmd = syrthes_ensight + ' -m ' + '"'+mesh_path+'"' + ' -r ' + '"'+resu_path+'"' + ' -o ' + '"'+output+'"'
elif mode == 'med':
# Execute syrthes -> med tool
sys.stdout.write(' .syrthes --> med.. \n')
cmd = syrthes_med + ' -m ' + '"'+mesh_path+'"' + ' -r ' + '"'+resu_path+'"' + ' -o ' + '"'+output+ '.med"'
sys.stdout.write(' --> ' + cmd +'\n')
try:
os.chdir(self.post_dir)
if self.echo:
retval = os.system(cmd + ' >> ' + self.logfile)
else:
retval = os.system(cmd)
os.chdir(self.exec_dir)
except:
err = ' Cannot execute tool to convert results into post-processing format\n'
err += ' -> Error !\n'
sys.stdout.write(err)
return 1
# rdt file
if (os.path.isfile(rdt_path)):
if mode == 'ens':
# Execute syrthes -> ensight tool
sys.stdout.write(' .syrthes (.rdt) --> ensight... \n')
cmd = syrthes_ensight + ' -m ' + '"'+mesh_path+'"' + ' -r ' + '"'+rdt_path+'"' + ' -o ' + '"'+outputrdt+'"'
elif mode == 'med':
# Execute syrthes -> med tool
sys.stdout.write(' .syrthes --> med.. \n')
cmd = syrthes_med + ' -m ' + '"'+mesh_path+'"' + ' -r ' + '"'+rdt_path+'"' + ' -o ' + '"'+outputrdt + '.med"'
sys.stdout.write(' --> ' + cmd +'\n')
try:
os.chdir(self.post_dir)
if self.echo:
retval = os.system(cmd + ' >> ' + self.logfile)
else:
retval = os.system(cmd)
os.chdir(self.exec_dir)
except:
err = ' Cannot execute tool to convert unstationary results into post-processing format\n'
err += ' -> Error !\n'
sys.stdout.write(err)
return 1
return retval
#---------------------------------------------------------------------------
def save_results(self, save_dir = None, horodat = True, overwrite = False):
if save_dir == None or len(save_dir) == 0:
save_dir = os.path.join(os.getcwd(), "SAVE.SYR")
if horodat == True:
now = datetime.datetime.now()
save_dir += "." + now.strftime('%m%d%H%M')
if os.path.isdir(save_dir):
if overwrite == False:
err = ' Directory to store results is already existing.\n'
err += save_dir
err += ' Do not overwrite existing data !\n'
sys.stderr.write(err)
return 1
else:
shutil.rmtree(save_dir)
try:
os.mkdir(save_dir)
except:
err = ' Cannot create directory to save Syrthes result.\n'
err += ' -> Stop this step !\n'
sys.stderr.write(err)
return 1
# Copy files
ls = os.listdir(self.exec_dir)
exclude = ['tmp.data', 'syrthes', 'syrthes.py', 'Makefile', 'POST', 'PART']
exclude += fnmatch.filter(ls, '*~')
for e in exclude:
if e in ls:
ls.remove(e)
for l in ls:
src = os.path.join(self.exec_dir, l)
if os.path.isfile(src) and not os.path.islink(src):
dst = os.path.join(save_dir, l)
shutil.copy2(src, dst)
if os.path.isdir(src) and not os.path.islink(src):
dst = os.path.join(save_dir, l)
shutil.copytree(src, dst, symlinks = False)
if self.post_dir != None:
try:
shutil.copytree(self.post_dir, os.path.join(save_dir, 'POST'),
symlinks = False)
except:
pass
if self.part_dir != None:
try:
shutil.copytree(self.part_dir, os.path.join(save_dir, 'PART'),
symlinks = False)
except:
pass
# Sucessful execution
return 0
#---------------------------------------------------------------------------
def dump(self):
print "\n SyrthesCase summary:\n"
print " Name = ", self.name
print " Data file = ", self.data_file
print " Update Data file = ", self.update_datafile
print " Do preprocessing = ", str(self.prepro)
print " Debug = ", str(self.debug)
print " Case dir. = ", self.case_dir
print " Execution dir. = ", self.exec_dir
print " Data dir. = ", self.data_dir
print " Source dir. = ", self.src_dir
print " Post dir. = ", self.post_dir
if self.part_dir != None:
print " Part dir. = ", self.part_dir
print "\n Conduction mesh dir. = ", self.c_mesh_dir
print " Conduction mesh name = ", self.c_mesh_name
if self.r_mesh_name != None and len(self.r_mesh_name) > 0:
print " Radiative mesh dir. = ", self.r_mesh_dir
print " Radiative mesh name = ", self.r_mesh_name
print "\n Total num. of processes = ", str(self.n_procs)
if self.n_procs_ray > 0:
print " Num. of processes for radiative transfer = ", str(self.n_procs_ray)
if self.echo == True:
print " Logfile name = ", self.logfile
print " Echo = ", str(self.echo)
print " Parallel run = ", str(self.parall)
print " Do preprocessing = ", str(self.prepro)
if self.param != None:
self.param.dump()
#-------------------------------------------------------------------------------
# Definition of a class for managing Syrthes parameters
#-------------------------------------------------------------------------------
class SyrthesParam:
def __init__(self, name = "syrthes.data"):
"""
Initialize the structure for a Syrthes computation
"""
self.name = os.path.basename(name) # parameter filename
self.c_mesh_name = None # conduction mesh name
# (only *.syr files are accepted)
self.c_mesh_prefix = None
self.c_mesh_suffix = None
self.r_mesh_name = None
self.r_mesh_prefix = None
self.r_mesh_suffix = None
# isabelle
self.result_name = None
self.result_file = None
self.restart_file = ''
self.restart = False
self.coupling = False
self.interpreted_func = False
# Read param file
try:
fdata = open(name, 'r')
except:
err = '\n Unable to open the SYRTHES data file ' + name + '\n -> Error !\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
coupl_apps = []
initkwd = fdata.readlines()
# Delete comment lines
kwds = []
[kwds.append(ch.strip()) for ch in initkwd if ch[0:1]!='/']
# Scan param file
for kw in kwds:
kws = kw.split("=")
k = kws[0].strip()
if k == "MAILLAGE CONDUCTION":
self.c_mesh_name = kws[1].strip().replace("\\", "/")
elif k == "MAILLAGE RAYONNEMENT":
self.r_mesh_name = kws[1].strip().replace("\\", "/")
elif k == "PREFIXE DU RESULTAT PRECEDENT POUR SUITE DE CALCUL":
self.restart_file = kws[1].strip().replace("\\", "/")
elif k == "PREFIXE DES FICHIERS RESULTATS":
self.result_name = kws[1].strip().replace("\\", "/")
elif k == "CLIM":
kk = kws[1].strip()
kk = kk.strip('0123456789_')
kk = kk.split()
if kk[0] == "COUPLAGE_SURF_FLUIDE":
self.coupling = True
elif kk[0] == "COUPLAGE_VOL_FLUIDE":
self.coupling = True
elif k == "SUITE DE CALCUL":
if kws[1].strip() == 'OUI':
self.restart = True
elif k.count('_FCT') > 0:
self.interpreted_func = True
# Treatment of the conductive mesh name
if len(self.c_mesh_name) == 0 or self.c_mesh_name == None:
err = '\n Conduction mesh name is not specified.\n' \
' -> Error !\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
self.c_mesh_prefix = os.path.basename(self.c_mesh_name)
self.c_mesh_suffix = self.c_mesh_name[len(self.c_mesh_name)-4:]
if self.c_mesh_suffix != ".syr":
err = '\n Invivalid mesh file format.\n' \
' Only SYRTHES format ".syr" is allowed' \
' If not, convert your format with SYRTHES tool "convert2syrthes"\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
# Treatment of the radiative mesh name
if self.r_mesh_name != None and len(self.r_mesh_name) > 0:
self.r_mesh_prefix = os.path.basename(self.r_mesh_name)
self.r_mesh_suffix = self.r_mesh_name[len(self.r_mesh_name)-4:]
if self.r_mesh_suffix != ".syr":
err = '\n Invivalid mesh file format.\n' \
' Only SYRTHES format ".syr" is allowed' \
' If not, convert your format with SYRTHES tool "convert2syrthes"\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
#isabelle
# Treatment of the result name
if self.result_name == None or len(self.result_name) == 0:
err = '\n Results prefix is not specified.\n' \
' -> Error !\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
# self.restart_file += '.res'
fdata.close()
#---------------------------------------------------------------------------
def update(self, n_procs, c_mesh_abspath, r_mesh_abspath, restart_abspath,
new_filename = "tmp.data"):
# Read param file
try:
fdata = open(self.name, 'r')
except:
err = '\n Unable to open the SYRTHES data file' + self.name
err += '\n -> Error !\n'
sys.stderr.write(err)
return 1
new_fdata = open(new_filename, 'w')
initkwd = fdata.readlines()
# Delete comment lines
kwds = []
[kwds.append(ch.strip()) for ch in initkwd if ch[0:1]!='/']
# Scan param file
for i in range(len(kwds)):
kw = kwds[i]
kws = kw.split("=")
k = kws[0].strip()
if k == "MAILLAGE CONDUCTION":
kws[1] = c_mesh_abspath
kws[0] += '='
kwds[i] = " ".join(kws)
elif k == "MAILLAGE RAYONNEMENT" and r_mesh_abspath != None:
kws[1] = r_mesh_abspath
kws[0] += '='
kwds[i] = " ".join(kws)
elif self.restart == True and k == "PREFIXE DU RESULTAT PRECEDENT POUR SUITE DE CALCUL":
kws[1] = restart_abspath
kws[0] += '='
kwds[i] = " ".join(kws)
elif k == "PREFIXE DES FICHIERS RESULTATS":
init_name = kws[1].strip()
# isabelle
if n_procs > 1 or self.coupling == True:
init_name = os.path.basename(init_name)
if n_procs > 1:
kws[1] = os.path.join('PART', init_name)
else:
kws[1] = init_name
kws[0] += '='
kwds[i] = " ".join(kws)
for kw in kwds:
new_fdata.write(kw)
new_fdata.write('\n')
fdata.close()
new_fdata.close()
return 0
#---------------------------------------------------------------------------
def dump(self):
print "\n SyrthesParam summary"
print " Param file name = ", self.name
print " Conduction mesh name = ", self.c_mesh_name
print " Radiation mesh name = ", self.r_mesh_name
print " Result prefix. = ", self.result_name
if self.restart == True:
print " Restart file = ", self.restart_file
print " Restart = ", str(self.restart)
print " Coupling = ", str(self.coupling)
print " Interpreted functions = ", str(self.interpreted_func)
print ""
# ***********************
# END OF CLASS DEFINITION
# ***********************
#***************************************************************************************
def create_syrcase(casedir):
#***************************************************************************************
retval = 0
# Check syrthes environment and set paths
if s4home == None:
retval = check_and_load_env()
if retval != 0:
err = '\n Error during checking and loading environment.\n'
sys.stderr.write(err)
return 1
if casedir == None or len(casedir) == 0:
err = '\n No path defined for creating SYRTHES4 case!\n -> Error !\n'
sys.stdout.write(err)
return 1
# Call shell script to create a new case
try:
s4case = os.path.join(s4home, 'bin', 'syrthes4_create_case')
subprocess.Popen([s4case, casedir]).communicate()
except:
err = ' -> Error !\n Cannot create syrthes case directory.\n'
sys.stderr.write(err)
return 1
return retval
#-------------------------------------------------------------------------------
# Processes the passed command line arguments and defined its relative syrthes
# case object
#-------------------------------------------------------------------------------
def process_cmd_line(argv):
"""
Processes the passed command line arguments.
"""
# Parse command line
parser = OptionParser(usage="usage: %prog 4.0 [options].\nType %prog -h")
parser.add_option("-d", "--data",
action="store", type="string",
dest="data_file",
help="Name of the SYRTHES data file")
parser.add_option("-n", "--nbprocs",
action="store", type="int",
dest="n_procs",
help="Number of processors for SYRTHES computation")
parser.add_option("-t", "--toolpart",
action="store", type="string",
dest="part_tool_name",
help="Tool for partitionning [metis] or [scotch]")
parser.add_option("-r",
action="store", type="int",
dest="n_procs_r",
help="Number of processors for SYRTHES radiation computation")
parser.add_option("--name",
action="store", type="string",
dest="syr_name",
help="List of coupled app. codes")
parser.add_option("-l", "--log",
action="store", type="string",
dest="logfile",
help="Name of the execution log file")
parser.add_option("-p","--no-prepro",
action="store_false",
dest="prepro",
help="Don't run the SYRTHES pre-processor")
parser.add_option("-v","--visu",
action="store", type="string",
dest="post_mode",
help="Define postprocessing format [ensight, med]")
parser.add_option("-g","--debug",
action="store_true",
dest="debug",
help="Run SYRTHES in debug")
parser.add_option("--exec-dir",
action="store", type="string",
dest="exec_dir",
help="Execution directory (default: current directory)")
parser.add_option("--data-dir",
action="store", type="string",
dest="data_dir",
help="Data directory (default: current directory)")
parser.add_option("--src-dir",
action="store", type="string",
dest="src_dir",
help="Source directory (default: current directory)")
parser.set_defaults(n_procs=1)
parser.set_defaults(n_procs_r=-1)
parser.set_defaults(part_tool_name="metis")
parser.set_defaults(syr_name="SYR")
parser.set_defaults(prepro=True)
parser.set_defaults(post_mode=None)
parser.set_defaults(debug=False)
parser.set_defaults(exec_dir=None)
parser.set_defaults(data_dir=None)
parser.set_defaults(src_dir=None)
(options, args) = parser.parse_args(argv)
# Error management
if not options.data_file:
parser.print_help()
err = "\n Incorrect command line definition.\n Define a data file.\n"
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
if not os.path.isfile(options.data_file):
parser.print_help()
err = '\n You must define the name of the data file\n' \
' Usage : syrthes.py -n nb_proc -d syrthes.data.syd\n' \
' Or name of data file with space: \n' \
' Usage : syrthes.py -n nb_proc -d "syrthes data syd"\n\n'
err += ' ' + options.data_file + ' is not a valid file.\n\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
if int(options.n_procs) < 1:
parser.print_help()
err = '\n You have to define the number of processors : -n [1..n]\n' \
' Usage : syrthes.py -n nb_proc -d syrthes.data\n' \
' Or name of data file with space: \n' \
' Usage : syrthes.py -n nb_proc -d "syrthes data syd"\n\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
if options.post_mode != None:
if options.post_mode == "med" or options.post_mode == "MED":
post_mode = 'med'
elif options.post_mode == "ens" or options.post_mode == "ensight" or options.post_mode == "ENSIGHT":
post_mode = 'ens'
else:
parser.print_help()
err = '\n Incorrect argument for post-processing mode\n'
err += ' Usage : syrthes.py -v ens\n'
err += ' Usage : syrthes.py -v ensight\n'
err += ' Usage : syrthes.py -v med\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
else:
post_mode = None
# Create a new syrthes case object and initialize by default
syr_case = SyrthesCase(name = options.syr_name,
data_file = options.data_file,
data_dir = options.data_dir,
exec_dir = options.exec_dir,
src_dir = options.src_dir,
n_procs = options.n_procs,
n_procs_ray = options.n_procs_r,
part_tool_name = options.part_tool_name,
post_mode = post_mode,
debug = options.debug,
prepro = options.prepro)
# Update syrthes case parameters
if options.logfile:
syr_case.set_logfile(options.logfile)
if syr_case.n_procs_ray > syr_case.n_procs:
err = '\n Number of processors for radiation must be less than the' \
' total number of processors : -r [1..n]\n' \
' Usage : syrthes.py -n nb_proc -d syrthes.data -r nb_proc_rad\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
return syr_case
#***************************************************************************************
def read_syrthes_param(data_file = "syrthes.data"):
#***************************************************************************************
return SyrthesParam(name = data_file)
#***************************************************************************************
def build_syrthes(parall = True, cfd_coupling = False, fname = None,
debug = False, srcdir = None, destdir = None):
#***************************************************************************************
# Display comment on the current step
sys.stdout.write(' Building the executable file syrthes.. \n')
call_dir = os.getcwd()
if srcdir != None:
if not os.path.isdir(srcdir):
err = " " + srcdir + " is not a valid directory !"
sys.stderr.write(err)
return 1
os.chdir(srcdir)
# Check if Makefile is in the current working directory
makefile=os.path.join(os.getcwd(), "Makefile")
if not os.path.isfile(makefile):
err = ' Makefile not found in the current working directory: ' + os.getcwd()
sys.stderr.write(err)
return 1
# Output file
if fname != None:
logfname = os.path.abspath(fname)
log = open(logfname, 'w')
# Append command line
cmd='make'
if parall == False and cfd_coupling == False:
cmd += ' MPI=no'
if cfd_coupling == True:
cmd += ' CFD=yes'
if debug == True:
cmd += ' DEBUG=yes'
if fname != None:
cmd += ' 2>&1 >| ' + logfname
retval = 0
try:
retval = os.system(cmd)
except:
sys.stderr.write('\n Error during the compilation stage\n')
retval = 1
else:
if retval != 0:
sys.stderr.write('\n Error during the compilation stage\n')
if fname != None:
log.close()
if retval != 1 and destdir != None:
if not os.path.isdir(destdir):
sys.stderr.write('\n ' + destdir + ' is not a valid directory !')
retval = 1
else:
if destdir != os.getcwd():
exec_name = os.path.join(destdir, "syrthes")
shutil.move(os.path.abspath("syrthes"), exec_name)
os.chdir(call_dir)
if retval == 0:
sys.stdout.write('\n ***** SYRTHES compilation and link completed *****\n')
return retval
#***************************************************************************************
def check_and_create_dir(dirname):
#***************************************************************************************
retval = 0
if dirname == None or len(dirname) == 0:
err = '\n No name defined for the directory to create!\n -> Error !\n'
sys.stdout.write(err)
return 1
else:
if os.path.exists(dirname) == False:
try:
os.mkdir(dirname, 0755)
return 0
except:
err = '\n -> Error !\n Unable to create ' + dirname + ' directory.\n'
sys.stderr.write(err)
return 1
elif not os.path.isdir(dirname):
err = ' -> Error !\n A regular file named ' + dirname + \
' is existing.\n' + ' Unable to create the directory.\n'
sys.stderr.write(err)
return 1
elif os.access(dirname, os.W_OK) == False:
err = ' -> Error !\n Cannot write into existing directory: ' + dirname + '\n'
sys.stderr.write(err)
return 1
return retval
#***************************************************************************************
def check_and_load_env():
#***************************************************************************************
global s4home, arch, mpidir
global syrthes_pp, syrthes_ppfonc, syrthes_post, syrthes_ensight, syrthes_med
# Check SYRTHES is in the $PATH
if s4home == None:
try:
out = subprocess.Popen(['which', 'syrthes4_create_case'],
stdout=subprocess.PIPE).communicate()[0]
s4bin = os.path.dirname(out)
s4home = os.path.abspath(os.path.join(s4bin,'..'))
except:
err = ' -> Error !\n Cannot find syrthes home directory.\n'
sys.stderr.write(err)
return 1
# Load environnement
sys.stdout.write(' SYRTHES4 home directory: ' + s4home + '\n')
# Find which MPI to use
if mpidir == None :
try:
fd = open(os.path.join(s4home, 'bin', 'syrthes.profile'), 'r')
content = fd.readlines()
matches = fnmatch.filter(content, 'SYRTHES4_MPIPATH*')
last_match = matches[len(matches)-1]
mpidir = re.split('=', re.split('\n', last_match)[0])[1]
fd.close()
except:
err = ' -> Error !\n Cannot find a MPI librairy.\n'
sys.stderr.write(err)
return 1
sys.stdout.write(' MPI home directory: ' + mpidir + '\n')
# Define syrthes directories
syrthes_pp = os.path.join(s4home, 'bin','syrthes-pp')
syrthes_ppfonc = os.path.join(s4home, 'bin', 'syrthes-ppfunc')
syrthes_post = os.path.join(s4home, 'bin', 'syrthes-post')
syrthes_ensight = os.path.join(s4home, 'bin', 'syrthes4ensight')
syrthes_med = os.path.join(s4home, 'bin', 'syrthes4med30')
return 0
#***************************************************************************************
def main(argv):
#***************************************************************************************
# Check syrthes environment and set paths
retval = check_and_load_env()
if retval != 0:
err = '\n Error during checking and loading environment.\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
# Build a new syrthes case object relative to the command line
syr_case = process_cmd_line(argv)
# Read data file and store parameters
syr_case.read_data_file()
# Initialize output file if needed
syr_case.logfile_init()
# Prepare SYRTHES execution
# -------------------------
print ""
print " -----------------------------------"
print " Prepare SYRTHES execution directory"
print " -----------------------------------"
print ""
retval = syr_case.prepare_run()
if retval != 0:
err = '\n Error during the prepration step (errno: '
err += str(retval) + '\n'
sys.stderr.write(err)
sys.exit('Stop Syrthes execution.')
# Sumary of the parameters
syr_case.dump()
# SYRTHES preprocessing
# ---------------------
# Pre-processing (only if Syrthes computation is done in parallel)
retval = syr_case.preprocessing()
if retval != 0:
sys.stderr.write('\n Error during the preprocessing step\n')
sys.exit('Stop Syrthes execution.')
# SYRTHES execution
# -----------------
print ""
print " -------------------------"
print " Start SYRTHES computation"
print " -------------------------"
print ""
# Run Syrthes
retval = syr_case.run()
if retval != 0:
sys.stderr.write('\n Error while running syrthes\n')
sys.exit('Stop Syrthes execution.')
else:
sys.stdout.write('\n ***** Successful execution ***** \n\n')
# Post-processing
if syr_case.post_mode != None:
retval = syr_case.postprocessing(mode = syr_case.post_mode)
if retval != 0:
sys.stderr.write('\n Error while post-processing result files.\n')
sys.exit('Stop Syrthes execution.')
else:
sys.stdout.write(' -> Ok\n')
sys.stdout.write("\n *** End ***\n")
if __name__ == "__main__":
main(sys.argv[1:])
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